The aim of this study was to develop techniques to sterilise the surface of silica gels containing encapsulated cells and the liquid broth they were immersed in, so that the observed metabolic activities could be unambiguously assigned to fully encapsulated cells. Gel surfaces were sterilised by UV-irradiation daily. The surfaces of the gels and the overlaying medium remained sterile for 20 days following irradiation, as demonstrated by the lack of visible surface growth and viable cells in the medium. We report the encapsulation of a viable, metabolically active, aerobic fungus Penicillium chrysogenum, and the aerobic Gram-positive bacterium Streptomyces rimosus in gels derived from aqueous silica sols. Carbohydrate consumption (catabolism) and antibiotic biosynthesis (penicillin or oxytetracycline) (anabolism) were monitored in both cultures, demonstrating that the encapsulated cells remained viable within the gel matrix. This demonstrates that the silica gels are sufficiently porous to sustain metabolic activities of aerobic cells, which require the diffusion of oxygen and other substrates within the gel's nanopore network.